when baking normals, do I have to set shading to smooth or flat for the low mesh?
A tangent space normal map is a bake of normals relative to the low poly's normals.  Whenever you make a tangent space normal map, it is going to take your existing normals, whether they're flat shaded or smooth shaded (or custom split normals, for that matter), and bake them into your normal map.
So I think you just have a bit of a misunderstanding of what a tangent space normal map is.  You shouldn't be looking at your baked image to judge a normal map-- it can't be judged on the basis of the image alone.  You should be judging it on the mesh for which it was built.
Now, it should be said, there is someplace where it's important whether your low poly is smooth shaded or flat shaded or something else.  That's because whenever Blender bakes anything, it looks in the direction of the baking normals to figure out what to bake.  So, for example, if you bevel a cube, and then bake to a flat-shaded cube, you'll find that some bake samples never actually hit the high poly.  Unless you know really well what you're doing, you generally want a smooth-shaded low poly that completely encloses your high poly.
It's not very clear exactly why you want your normal map to somehow be independent of your low poly's normals.  I think there's probably some misunderstanding of what a normal map is, or what the colors mean.  But if you're really sure that you don't want your normal map to depend on your low poly's normals, you might consider baking an object-space normal map instead.  Object space normal maps are stored relative to object space, rather than relative to the sample's normal (which turns into the Z axis for the tangent space.)  However, object space normal maps will still be affected by your normals in that the low poly normals will still determine which way the rays shoot from the low poly (or cage) to hit the high poly.  Object space normal maps are not any good for deforming geometry, which is why tangent space normal maps are seen more frequently.